Research workbench
Crystal structure of E. cloacae 3,4-dihydroxybenzoic acid decarboxylase (aroy) reconstituted with prfmn
Analyse Crystal structure of E. cloacae 3,4-dihydroxybenzoic acid decarboxylase (aroy)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O3N
- Type
- protein
- Length
- 976 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3,4-dihydroxybenzoate decarboxylase
- UniProt
- B2DCZ6
- Ligands
- 4LU, MN, NA
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3,4-dihydroxybenzoate decarboxylase | protein | 488 | 28% helix, 25% strand | B2DCZ6 |
Ligands and binding sites
- 4LU · 1-deoxy-5-O-phosphono-1-(3,3,4,5-tetramethyl-9,11-dioxo-2,3,8,9,10,11-hexahydro-7H-quinolino[1,8-fg]pteridin-12-ium-7-yl)-D-ribitol · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 621 | 0.79 | 0.84 | 64 | GOL, 4LU |
| 2 | 579 | 0.78 | 0.84 | 61 | GOL, 4LU |
| 3 | 460 | 0.57 | 0.74 | 49 | empty |
| 4 | 59 | 0.50 | 0.86 | 18 | empty |
| 5 | 79 | 0.33 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 3985 Ų buried · 47 hydrogen bonds · protein-protein
Compared structures
- 5O3N · Crystal structure of E. cloacae 3,4-dihydroxybenzoic acid decarboxylase (AroY)… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt B2DCZ6
- Elsewhere: RCSB PDB 5O3N · PDBe 5O3N · UniProt B2DCZ6
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